Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

Jami, Elie; Mizrahi, Itzhak

doi:10.1371/journal.pone.0033306

Cited by 463 publications

(388 citation statements)

References 30 publications

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“…1) (R 2 = 0.94). Based on the strength of this result, we tested whether this scaling law holds at greater scales of N. We used published estimates for N and N max from the human gut (27,28), the cow rumen (29,30), the global ocean (nonsediment), and Earth (6,7,31,32). In each case, we found that N max fell within the 95% prediction intervals of the dominance scaling law (Fig.…”

Section: Predicted Scaling Of Species Richness (S)mentioning

confidence: 95%

“…Cow rumen. The most dominant taxonomic unit (based on 97% sequence similarity in 16S rRNA reads) in the cow rumen is typically a member of the Provotella genus and has been reported to account for about 1.5-2.0% of 16S rRNA gene reads in a sample (29,30). Assuming there are about 10 15 microbial cells in the cow rumen (29,30) and if these percentages are reflective of community-wide relative dominance (D BP ), then N max of the cow rumen would be in the range of 1.5·10 14 to 2·10 14 .…”

Section: Locey and Lennonmentioning

confidence: 99%

See 1 more Smart Citation

Scaling laws predict global microbial diversity

Locey

Lennon

2016

Proc. Natl. Acad. Sci. U.S.A.

823

337

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Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ∼35,000 sites and ∼5.6·10 6 species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we show similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upward of 1 trillion (10 12 ) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome.biodiversity | microbiology | macroecology | microbiome | rare biosphere T he understanding of microbial biodiversity has rapidly transformed over the past decade. High-throughput sequencing and bioinformatics have expanded the catalog of microbial taxa by orders of magnitude, whereas the unearthing of new phyla is reshaping the tree of life (1-3). At the same time, discoveries of novel forms of metabolism have provided insight into how microbes persist in virtually all aquatic, terrestrial, engineered, and host-associated ecosystems (4, 5). However, this period of discovery has uncovered few, if any, general rules for predicting microbial biodiversity at scales of abundance that characterize, for example, the ∼10 14 cells of bacteria that inhabit a single human or the ∼10 30 cells of bacteria and archaea estimated to inhabit Earth (6, 7). Such findings would aid the estimation of global species richness and reveal whether theories of biodiversity hold across all scales of abundance and whether socalled law-like patterns of biodiversity span the tree of life.A primary goal of ecology and biodiversity theory is to predict diversity, commonness, and rarity across evolutionarily distant taxa and scales of space, time, and abundance (8-10). This goal can hardly be achieved without accounting for the most abundant, widespread, and metabolically, taxonomically, and functionally diverse organisms on Earth (i.e., microorganisms). However, tests of biodiversity theory rarely include both microbial and macrobial datasets. At the same time, the study of microbial ecology has yet to uncover quantitative relationships that predict diversity, commonness, and rarity at the scale of host microbiomes and beyond. These unexplored opportunities leave the understanding of biodiversity limited to the most conspicuous species of plants and animals. This lack of synthesi...

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Section: Predicted Scaling Of Species Richness (S)mentioning

confidence: 95%

Section: Locey and Lennonmentioning

confidence: 99%

Scaling laws predict global microbial diversity

Locey

Lennon

2016

Proc. Natl. Acad. Sci. U.S.A.

823

337

View full text Add to dashboard Cite

show abstract

“…Although rumen microbial community composition varies with diet and host, a 'core microbiome' is found across a wide geographical range [25,31,58]. Ruminants depend on these rumen microorganisms to digest nutritional components in feedstuffs and to convert them into proteins, carbohydrates, VFAs and gases [52].…”

Section: Core Prokaryotic Communities In the Rumenmentioning

confidence: 99%

Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau

Xue

Chen

Zhao

et al. 2017

Systematic and Applied Microbiology

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“…In order to identify the kind and dominance of rumen microorganisms, 16 Holstein cows were bred in the same conditions, then DNA was extracted from rumen microorganisms and applied with a pyrosequencing technique in which V2 and V3 regions of 16s rRNA were amplified. As result, it was found that Bacteroidetes existed in the ratio of 51%, Firmicutes 43%, Proteobacteria 5.21%, Actinobacteria 0.87%, and Tenericutes 0.68% [44].…”

Section: Ruminant Microorganismsmentioning

confidence: 91%

Use of Cellulose and Recent Research into Butyrate

Yeo¹,

Choi²,

Cho³

2012

Journal of Life Science

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On earth, there are about 5,400 kinds of mammals, of which about 1,000 kinds are herbivores. Among herbivores, about 250 kinds are known to be ruminants. As for cattle and sheep, which are ruminants, fermentation takes places mainly in their rumen; in contrast, for pigs and men, which are non-ruminants, fermentation takes place mainly in their caecum, colon, and rectum. As for the kind and dominance of rumen microorganisms, Bacteroidetes account for 51% and Firmicutes for 43%. As for the dominance of the large intestine microorganisms in men, Firmicutes account for 65% and Bacteroidetes for 25%. Cell wall components are decomposed by microorganisms, and short chain fatty acids (SCFAs) are generated through fermentation; the ratio of acetate, propionate, and butyrate generate is 60:25:15. Butyrate absorbed through the primary butyrate transporter MCT1 (mono carboxylate transports-1) in the intestines activates such SCFA receptors as GPR43 and GPR41. Butyrate has a strong anti-tumorigenic function. Butyrate is characterized by the fact that it has an effect on many cancer cells, contributes to the coordination of functions in the cells, and induces cancer apoptosis. Butyrate activates caspase but inhibits the activity of HDAC (histone deacetylase), so as to induce apoptosis. In addition, it increases p53 expression, so as to induce cell cycle arrest and apoptosis. Anti-inflammation actions of SCFA include the reduction of IL-8 expression in intestinal epithelial cells, the inhibition of NO synthesis, and the restraint of the activity of NF-kB (nuclear factor kB), so as to suppress the occurrence of cancers caused by inflammation. Butyrate plays an important role in maintaining physiological functions of intestinal mucous membranes and is used as a cure for inflammatory bowel disease (IBD). Digestive organ of ruminant and mono-gastric animals Ruminants are referred to as so because of their rumination or special digestive organ (the stomach), in which cud can be chewed. Ruminants are the most advanced animals of ungulates and the most multiplied and prevalent throughout the world. They have a rumination, which is a very peculiar digestive organ and possibly enables them to have survived poor vegetation conditions, allowing them to flourish greatly. The stomach of all ruminants is divided into four compartments including the rumen, reticulum, omasum, and abomasums (of which rumen and reticulum are involved in rumination and called rumen). Rumination is a process in which food, once swallowed, is emitted back unto the mouth for re-chewing; of feeds returned into reticulum via rumen, those of which over a certain size will be returned again into rumen, accumulated, and regurgitated to the mouth. The regurgitated feeds will be smashed finely between molar teeth and mixed with saliva in the mouth, then returned to rumen for fermentation. Ruminants include cattle, sheep, goats, deer, musk deer, giraffes, and impalas.Pseudo-ruminants have a similar stomach to rumen in which microorganism fermentation takes place, but thei...

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Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

Cited by 463 publications

References 30 publications

Scaling laws predict global microbial diversity

Scaling laws predict global microbial diversity

Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau

Use of Cellulose and Recent Research into Butyrate

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